Description Usage Arguments Value References Examples
Perform enrichment of cell type signatures based on the full gene expression matrix.
1 | clustermole_enrichment(expr_mat, species, method = "gsva")
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expr_mat |
Expression matrix (logCPMs, logFPKMs, or logTPMs) with genes as rows and clusters/populations/samples as columns. |
species |
Species: |
method |
Enrichment method: |
A data frame of enrichment results.
Barbie, D., Tamayo, P., Boehm, J. et al. Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature 462, 108–112 (2009). doi: 10.1038/nature08460
Hänzelmann, S., Castelo, R. & Guinney, J. GSVA: Gene set variation analysis for microarray and RNA-Seq data. BMC Bioinformatics 14, 7 (2013). doi: 10.1186/1471-2105-14-7
Foroutan, M., Bhuva, D.D., Lyu, R. et al. Single sample scoring of molecular phenotypes. BMC Bioinformatics 19, 404 (2018). doi: 10.1186/s12859-018-2435-4
1 | # my_enrichment <- clustermole_enrichment(expr_mat = my_expr_mat, species = "hs")
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